Scottish and Irish, of uncertain origin.

Ninian has long been in use in northern England but is now almost entirely Scottish and Irish. It is in honour of St Ninian (c. 400 CE), a British monk who was educated in Rome. 

Ninian occurs very rarely in the 1841 Census of Aberdeenshire, with the equally very rare spellings of Ninnian and Niniam, although the latter may be a mis-transcription.